› 3od8

X-ray diffraction
2.4Å resolution

Human PARP-1 zinc finger 1 (Zn1) bound to DNA

Released:
DOI: 10.2210/pdb3od8/pdb
PDB entry 3od8 coloured by chain, front view.
PDB entry 3od8 coloured by chain, side view.
PDB entry 3od8 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structures of poly(ADP-ribose) polymerase-1 (PARP-1) zinc fingers bound to DNA: structural and functional insights into DNA-dependent PARP-1 activity.
Langelier MF, Planck JL, Roy S, Pascal JM
J Biol Chem 286 10690-701 (2011)
PMID: 21233213

Function and Biology Details

Reaction catalysed: 
NAD(+) + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116641 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Poly [ADP-ribose] polymerase 1, processed N-terminus Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 116 amino acids
Theoretical weight: 13.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P09874 (Residues: 2-96; Coverage: 9%)
Gene names: ADPRT, PARP1, PPOL
Sequence domains: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
Structure domains: Zinc finger, PARP-type
5'-D(*GP*CP*CP*GP*CP*TP*TP*GP*GP*G)-3' Chains: I, K, M, O
Molecule details ›
Chains: I, K, M, O
Length: 10 nucleotides
Theoretical weight: 3.08 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*CP*CP*CP*AP*AP*GP*CP*GP*GP*C)-3' Chains: J, L, N, P
Molecule details ›
Chains: J, L, N, P
Length: 10 nucleotides
Theoretical weight: 3.01 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 8 x ZN
1 modified residue:
Ligand MSE 40 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P21
Unit cell:
a: 63.219Å b: 107.696Å c: 86.138Å
α: 90° β: 100.2° γ: 90°
R-values:
R R work R free
0.194 0.192 0.241
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

50 review citations

New insights into the molecular and cellular functions of poly(ADP-ribose) and PARPs.
Gibson et al. (2012)
49 more

7 mentions without citation

PARP-1 mechanism for coupling DNA damage detection to poly(ADP-ribose) synthesis.
Langelier et al. (2013)
6 more